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README.md

Leucippus

Leucippus is a Electron Microscopy analysis tool that is designed as a plugin for the ImageJ tool stack that runs in the (Java Runtime Environment) JRE and works in conjunction with python.

Install

This installation guide assumes that you already have ImageJ installed and working. It is important that you have run ImageJ at least once before trying to install the plugin as the ImageJ plugin folder is not created until then. If you do not then you can find ImageJ available on many package managers.

Dependencies

To build and run Leucippus you need the following software:

  • Git
  • Make
  • python 2.7
  • numpy
  • scipy
  • python-opencv
  • python-networkx
  • jdk8 (javac 1.8)
  • ij.jar (ImageJ jar file)

Commands

If you are using apt for your package manager you can easily install all of these using the command:

sudo apt install git make python python-numpy python-scipy python-opencv python-networkx openjdk-8-jdk

If you are not using apt or you are using a virtual environment you will need to find the correct packages to build the code.

In order to build and install this repository you'll need to have run imageJ atleast once. To build Leucippus, navigate to your repository directory and use make. This will build and package the java classes and python code into a jar and zip file respectively. Then just use make install in order to place the files within the imageJ plugin.

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